text:
Why does it take so long to develop modern military jets?
In the 1960's, it took three years to produce a flying prototype of an aircraft that flew faster than anything before, was built out of a novel construction material, used a new type of fuel, and was incredibly advanced: the Lockheed A-12. Its successor the SR-71 was the first aircraft with stealth technology applied, and stayed in service for decades.

From the Wikipedia page of the A-12:

March 1959: a pre-design drawing differing from the final configuration
26 January 1960: order of 12 A-12 aircraft
25 April 1962: first flight of the prototype.

The F-35 program is a modern day jet platform program. It took 5 years to develop and build a winning prototype, and then 5 years for first flight of a production machine. It has been in the news for years for delays and cost overruns - latest problem is with the oxygen system.
From its Wikipedia:

The JSF development contract was signed on 16 November 1996,
26 October 2001 to Lockheed Martin, whose X-35 beat X-32
15 December 2006 F-35 first flight
In 2012, General Norton A. Schwartz decried the "foolishness" of reliance on computer models to arrive at the final design of aircraft before flight testing has found the problems that require changes in design.

So to the uninitiated, it seems like half a century ago, the awesomest plane on earth could be delivered for service three years after finalising design. The successor SR-71 was developed in 2 years, had the addition of the side chimes for reducing radar cross-section, and was so much ahead of its time that it could stay in service for decades. Now, it takes 10 years from contract sign to first flight of a production machine that remains experiencing design problems until the present day, and then a further 10 years to debug all problems.
The A-12 engineers faced very complicated problems as well, yet they could solve them in record time. What am I missing? Why does development take so much longer?
Edit
How about this one:

in 1972, the Air Staff selected General Dynamics' Model 401 and Northrop's P-600 for the follow-on prototype development and testing phase.
The first YF-16 was rolled out on 13 December 1973, and its 90-minute maiden flight was made at the Air Force Flight Test Center (AFFTC) at Edwards AFB, California, on 2 February 1974.

Update: the answer. -- Updated update: more would make the question too long, I've added an answer.
Multiple very good answers list the following:

Fewer types expected to take on more roles
Lack of competition
No urgency imposed by war
Therefore, no work force experienced in rapid solving of extremely complicated problems
Peace-time politics having to justify budget decisions to the voters.
Better testing and greater safety imposing more time demands.

All are very good points. The light attack aircraft with short development time is illustrative, as is this article in The Economist.
I still have great difficulty in accepting that:

A reason would be the complexity of the problem, which is very often quoted. All aerospace problems are extremely complex, that is nothing new. But now nobody can tackle them anymore? That was the basis of my question.
Having fewer airframe types saves cost and/or development time, this seems evidently incorrect. Pointed out in @Hephaestus Aetnaean's answer
It should cost twenty years to properly develop an aircraft. Upgrades during the life cycle, sure. On the number of lines of code as reason, here is some perspective. 8 Million Lines Of Code (MLOC) compares with Firefox and the Chevy Volt, 24 MLOC with Apache Open Office.

Update 2
Additional points are made below - by writing in big black letters. Not sure if that makes the point more valid.
Cost-wise, the F-35 indeed beats Augustine's law XVI. The article in The Economist from 2010 referenced above has the predicted F-35 in the plot, according to @Hephaestus Aetnaean the cost is even lower, just below the $10^8$ dollar line:

So the year in which all of the US defence budget can buy only one aircraft may be postponed from predicted 2054 to maybe 2074?
Development time wise (which is what the question is about), it is pointed out that F-35 development time is 2.5 times F-16 time. That is a big leap in a bit over two decades. Yes development time of European jets is long as well, perhaps due to smaller defence budget of smaller countries? Ironic that they are setting the standard in this.
Long software development time - has software engineering not developed methods to tackle large complicated problems? Especially where the problem - and solutions - increase incrementally? Does better testing and off-line simulation not allow for decoupling off of the project critical path, and therefore save time instead of requiring more? I opened up a question on Stack Exchange Software Engineering, and they mention that FireFox has 20 millon lines of code.
I don't want to knock the F-35, it's indeed an awesome platform. If it ends up a capable platform for a reasonable price, that is great and I wish all the best to pilots carrying out their mission in service of their country. And perhaps the long development time and multiple news items remain only a memory.
Update 3
Too long to include in a question edit, refer to my answer below.

I suggest moving this to the history stackexchange, as a full discussion requires a telling of military history.

@EricUrban we also have an aviation-history tag.

I think the SR-71 was not so much "ahead of its time" as that it was good enough at the limited set of jobs it did that there was no need for a replacement.  Though one could argue that it has mostly been replaced by something entirely different: satellites.

This question is interesting because the same seems true of almost ALL technology these days - while model lifecycles and scaling are fast, innovation is not...

Your timeline is a little short for the SR-71. Preliminary work on the A-12 (precursor to the SR-71) began in 1957.

Indeed. Although the wiki page for A-12 shows pre-design drawings in March 1959 indicating that the design was not yet frozen. Then 3 years later the prototype was flying. I'll amend the question.

I think a big part of the answer is that the looming threat of nuclear annihilation makes a good motivating factor.  Note that the aircraft you reference was developed as a spy plane, to carry out recon over the USSR.

There is a long way between a design drawing and an actual Mach 3.2 aircraft.

@jamesqf the role of the SR-71 is still performed, not by satellites (due to physical limits of imagery, cloud cover) but by the U2, which the SR was meant to replace.

Does the U2 not have a problem with being shot down anymore?

@Koyovis No, but the SR-71 wouldn't achieve that purpose anymore anyway.

I think the entire reason is "software".  You can't make an kid's app (that works) in 10 years.

Why is that? What makes software fundamendally different from other complicated problems?

Because the contractors are paid by the hours now.

I adde a fourth reason, seeing how unhappy you are with the answers. It is now spelled out, even though it was implicit in the other three reasons.

No I reckon they are all very good.

Read the book skunkworks. It's by a former director of the skunkworks at Lockheed who worked on the blackbird (as a thermodynamics specialist) and he talks about this issue, and he attributes a large percentage of the problem to bureaucracy and increased regulation. He feels like it's slowed innovation and increased red tape to get through to do ordinary things.

I find this an illustrative quote from the Wikipedia [A-12 article]{https://en.wikipedia.org/wiki/Lockheed_A-12}: The companies' respective track records proved decisive. Convair's work on the B-58 had been plagued with delays and cost overruns, whereas Lockheed had produced the U-2 on time and under budget. Where is Skunk Works now?

How about this one Do you mind clarifying your question?

Perhaps one rather direct way of thinking: the materials/technology are markedly more expensive than decades ago(?) -> less room for error -> mathematically, a consequence of the increased item cost(#1) and the relatively unchanged cost of employees/time(#2), the ratio of #2 you should devote to each #1 increases... i.e. what were before seen as small improvements [like wind tunnel testing] are now cost effective, since you can less afford later replacements, and because it's yet more vital this new technology defeat the old. Measure twice cut once for wood? Measure 8 times cut once for gold!

@JeopardyTempest. That's a difficult qualitative analysis. We also have powerful CFD and simulation tools that can give us a head start, before any hardware is built. Can even test 90% of material strength with finite element methods.

@HephaestusAetnaean Prototype was rolled out in 2 years. With novel fly-by-wire software, perhaps cause of crashes. Nowadays we can test it all concurrently without having to test it on the prototype anymore. Where is my error of reasoning?

@Koyovis, I certainly understand that it's a difficult qualitative analysis.  But are you saying that most of the time isn't spent in testing/refinement anymore, but that most of the time is in the initial design phase?

@JeopardyTempest I don't know. Between start of development of F-16 and that of F-35 were 20 years. Development time seems to have increased an order of magnitude in that time. More complexity and safety, but also more tools to help save time in the design and decouple design issues from the critical path.

@Koyovis Because the gov't uses no-compete, cost-plus contracts for them, so contractors can take as long and charge as much as they want, thanks to the US' view of military funding being of utmost importance.

@Koyovis - YF-16 was just an airframe+engine without any mission systems (quite different from the F-16A). Its equivalent would be the X-35, which also demoed the airframe+engine in a novel STOVL system. The X-35 was signed in 1996, flew in 2000, just four years. ----- F-16: 2 years for demo (1972-74), 4 years to first flight (1972-76), 8 years to service entry (1972-80) ---- F-35: 5 years for demo (1996-2001), 10 years to first flight (1996-2006), 19 years to service entry (1996-2015).

I'd just like to add that a famous aerospace engineer (my apologies I forgot his name)  said that "there are four dimensions to aircraft design: cost, efficiency, capability, and politics" Gives a humorous but quite accurate description to how fighter jets are produced today!

First of all, it took at least five years even back then, but your observation is absolutely correct. You  would need to go back one more decade to find a frontline fighter that was designed within two years.
The reasons are:

Urgency: Back then, the Cold War arms race forced both sides to continuously improve. Together with the advances in weapons and tactics, this meant that upgrading older airframes did not suffice.
A trained workforce: Experienced engineers back then had worked on a dozen new designs (or more), so they had developed a gut feeling how to design the next one. Today, one can be lucky to have brought a single one into the air within a lifetime.
Complexity: As aircraft become ever more expensive, their specs are mulled over for years. The time it takes to write today's specs is reflected in the sometimes contradicting demands put on a new design. Every new design has to be a Jack of all trades which will increase development time. A lot.
Culture: Today's culture is very risk-averse. Contrast that to the Fifties, when the F-100 went supersonic on its second test flight and went on to be involved into 889 accidents, causing the death of 324 pilots over its operational career. Design and testing was much less thorough, leaving more complicated effects like flutter or fatigue to chance and accepting others like dangerous stall characteristics. Today, we evaluate and test much more because we can and try to avoid mishaps at almost all cost. That takes time.

I can't stress the importance of the second point enough. When the first aerodynamic dataset for the TKF-90 was sent to the simulation guys at MBB, it was rejected because the coefficients were obviously "wrong". As it turned out, the guy in simulation had spent his entire career with Tornado data, so this was all he knew. In my time, I tried to lobby for a cheap design just to keep people trained, but got nowhere with the beancounters running the company. For them, every engineer was the same. In their eyes, experience can be judged by an engineer's degree and company-funded training is a waste of money. See, the training issue goes all the way up to the top! If even the bosses have little idea what it takes to design a good aircraft quickly, you get what we have today.
Note that complexity not only concerns the airframe. Modern programs are mostly multinational and spread over as many constituencies as possible. The amount of coordination of such an artificially increased workforce is immense. Also, testing all states of a complex airframe takes much more time and risk management means that quick trials are impossible. Back then, the strategy was mostly trial and error, whereas today every program is tested to death to avoid any failure.
Have you ever read Augustine's Laws? This is a great book with a lot of profound insights into the military aviation business. And when even the CEO of Lockheed cannot make a dent in the system even though he has demonstrated a deep understanding of its faults, you know how little can be changed.
Because you used the SR-71 as an example: This combines all points in the extreme.

After the U-2 incident and without working satellites, urgency was extreme. People worked almost around the clock to get the new design into operation. Contrast this with today where a flight test is postponed for the slightest risk. Delays? Who cares!
Kelly Johnson hand-picked the best engineers from the Burbank offices and had been working on Mach 3 designs for almost a decade before. Also, the most time-consuming detail of the Blackbird family of aircraft, their engine, was ready when he started. I remember from Ben Rich's autobiography that Kelly could predict the heat load of a shockwave with only a few degrees of error just by guessing back then. To develop this kind of experience takes a lot of wind tunnel data! And he had almost complete liberty to decide how to proceed. No beancounter dared to second-guess his decisions - performance was still more important than profits. Compare that with today …
The Blackbird family of aircraft was meant to do one thing only. Fly fast. No demands on turn rate, field length or a wide variety of external loads. Also no dozens of mission profiles, high and low, loiter and penetration, air superiority and bombing with one platform. That helped to get it out the door quickly.

That the Blackbird family was not replaced by something better was caused by … wait for it … the ever increasing cost of new designs. It simply was the last in a long line.

I like Augustine Law XII. So the answer might be that the guys with the brilliant solutions are not there anymore?

@Koyovis: This might indeed be a factor. The best minds are attracted by the most complex problems and hate being held back by dumber people of higher rank. Today's aviation industry is close to the perfect place to repel them.

Your comment about "every engineer was the same" is so so true in contracting. I was part of a team where management thought little of getting rid of experienced engineers at the drop of a hat just because next month's budget was slightly lower. Eventually it was my turn as a budget victim, and I knew that a few months later they would be on the market again, crying of the tech "skills gap", wondering what happened to all the skilled engineers. Of course, being a former employee was a black mark against you. We weren't even working on jets - we were doing logistics systems.

@RobertColumbia: And it works, in their eyes! I witnessed a program with a problem which required expert advice, but the recommended expert was too expensive, so just some engineer was hired. He failed. Five more were hired and failed, too. Ten more were hired and by chance, one of them realized what the problem was. Management congratulated themselves how successfully they had solved the problem. That they could had achieved the same at a small fraction of the time and expense never occurred to them.

Next time the bean counters try to contradict you, just show them this. :)

Would also have to add what no one has said: there's a hell of a lot more money in project delays than there used to be.  This has been covered in a lot of places but the film Why We Fight is as good a source as any.

then probably, in the fifties the management must have been much flater. perhaps even the engineers were not managed at all ? they just had carte blanche because of trust from the officers, and urgency.

@v.oddou: Certainly Kelly Johnson had. When upper management interfered, he let them know what his rules were in no uncertain way. This behaviour would be totally unacceptable for today's political correctness, but did get the job done. Much more important, however, was that the bosses were engineers themselves who understood the process, not beancounters like today.

There are quite a few reasons for this- technically speaking, the primary one is that the system complexity has increased tremendously. More systems mean more interfaces, more redundancies, meaning more chances of failure and more troubleshooting. The modern combat aircraft is expected to perform a wide variety of missions, which would've been performed by different aircraft in the past.
Modern combat aircraft are multirole (or omnirole, if you go by the French), expected to perform more things and better than their predecessors and last longer. Consider the case of the F-35. The aircraft is expected to perform roles performed by a variety of aircraft (F-16, A-10 and F/A-18) in different services. Compared to this, the primary mission of the SR-71 was simple- go fast undetected (fast being the primary one).
Added to this, the aircraft is expected to have systems integrated into it to enable it to be operated well into the future. Electronic systems are still a work in progress and its development costs are significant, easily eclipsing the cost involved in the development of airframe. In fact, the electronic system will be development long after the airframe is finalized, resulting in R&D costs right until the aircraft is fielded (and well after that) as the customer wants to cram as much systems as possible into the airframe.
The image below shows the type and number of combat aircraft in USAF service since the 1950s.

Aircraft in USAF service; image from math.andyou.com
This clearly shows the issue- fewer modern aircraft are expected to perform better than their more numerous predecessors and it is only expected to become more severe.
There is another thing that is not obvious from the graph- the number of suppliers available. For example, in 1960, you have the F-86 Sabre made by North American, F-84 Thunderjet made by the Republic Aviation, the F-89 Scorpion made by Northrop and F-106 Delta Dart made by Convair, and this is only a partial list. Today, if the USAF wants to buy a fighter, they got Lockheed (and Boeing by a thread) and nobody else.  There is no competition here.
As the selection pool decreases, it becomes more difficult for the buyer to enforce any fiscal discipline, especially when the contract is cost plus. Another thing is that the tendency to take risk goes down- no one wants the next one to go under by making a mistake when the costs outweigh the benefits. You have this situation where the last guy standing is sure that the government is going to fund him as much and as long no matter what the cost overruns are- simply because there is no plan 'B'.
There is another facet to this- if the development contracts are not continuous i.e. back to back, the knowledge of development of the systems have to be re-learned every time, resulting in more delays. It is easier to build on available knowledge base rather than learning something new. The people who worked on SR-71, for example, had already worked on A-12 Cygnus. Skills that are not updated continuously will perish easily, especially in aerospace, where the talent pool is rather small. So, don't be surprised if the next aircraft take more time and money to develop.

The A-12 Cygnus looks a lot like the SR-71 and was capable of high altitude flight (90,000 feet) at top speeds of over mach 3. You could almost argue the SR-71 was a refinement.

So to paraphrase, the F35 is a multifunction fax-printer-scanner-toaster-wafflemaker where historically up to five different aircraft might have been used for one purpose each.

I'm skeptical to believe that complexity is the main factor given that the SR71 was designed with drafting machines and the titanium to build it had to secretly be acquired from the USSR.

Agreed. The other guys also had very complex problems, and brilliant solutions.

@Koyovis They had hard math problems, with elegant engineering solutions. The F-35 is a significantly more complex problem with far more (literally!) moving parts to worry about. The extended state of a system increases exponentially as you add more features and that is a big challenge for engineering.

Something else to keep in mind is that the less planes that are made, the less automation takes place. I.E. it requires more human intervention, as opposed to a robot factory where hundreds/thousands of parts are being churned out in the same way everyday.

Wouldn't it be cheaper overall to build more single use aircraft rather than one multirole one that doesn't do any role well?

"F-89 corpion" Scorpion link is missing an S

@DavidFindlay Yes, and they learned that by making this plane.  It's not really exceptional at anything, and it needs to be.  It's probably the last manned fighter, so...

I don't really buy this, look at the Saab Gripen's development cycle. The difference while they made mistakes, they couldn't afford to be wasteful on the same scale as the F35 program. I don't think the USA is a good example at all actually. We should be looking at arms industries that aren't so heavily politicized and propped up by their government.

Either I can't find them, or there's no F-14 Tomcat in your picture. Why?

UPDATE:
I want to clarify/emphasize a few things in my answer.
#1: Ultimately, the core driver of development time is growing complexity.
More advanced threats means more advanced systems, which usually means more complexity.

Your opponent gets a bigger radar, so you need a bigger one to see him first. You add jammers to shorten his effective radar detection range; he switches to IR sensors to augment his radar; you have to reduce your IR signature (buried/insulated engines, serrated nozzles).
He coordinates with ground controllers and their huge radars; you jam his comms; he adds anti-jam functionality to his comms; you coordinate with AWACS to extend your own detection range and add standardized comms so everyone can talk to each other.
You go low to hide your radar signature in ground clutter; he adds Doppler filtering.
He gets IR missiles; you get IR jammers; he gets jam-resistant IR seekers; you get lasers to burn his seekers.
You build a more maneuverable fighter; he gets super-maneuverable dogfighting missiles that can lock on at extreme angles.

These advanced capabilities aren't optional. They're necessary for survival. Even more capability is required to actually execute a mission.

No missile approach and warning system? You might never see the missile coming.
No radar jammers, no laser IR jammers, no decoys? Then his missiles are more likely to hit.
No low probability of intercept functionality (radar and comms)? Then he could detect you from long range (rendering your stealth less useful) or jam your radar.
No ground-mapping modes? Then you have to spend more time in hostile air space looking for a target. Or you have to rely on someone else to find targets for you (now you need two aircraft).
No integrated ground targeting pod? Then you need an external pod, which is draggier and increases you RCS.
No stealth? No jamming? Have fun starring at long range radars and SAMs.
No jam-resistant comms? Have fun talking to yourself.

#2: So why not design everything incrementally?
Why not fly a quick n' dirty design, find the problems, and then fix it in the next block?
First, we still do that (to a degree). The F-22, F-35, and B-21 all have upgrade paths.
Second, that can be more expensive and time consuming that designing everything at once.

A \$1 flaw in design costs a \$10 in production and \$100 in the field. When aircraft are already so expensive, the flaws will also be expensive to fix.
When aircraft are so complex, purely serial design/development would take forever.
Low-rate production is inefficient/costly. Stopping production between blocks is even more costly.

But designing everything simultaneously is more complex (more balls to juggle).
So there's a balance between serial and concurrent development.
#3: Development time is counted differently

Better testing and greater safety imposing more time demands. - [from the updated question]

It's not only that modern testing is more stringent/complete/safe, but that modern development time is counted differently.

F-16 development time is longer than it appears because the F-16 essentially entered service before testing was complete. (Remember how the tail had to be enlarged by 25% to address deep stall? That fix didn't happen until Block 15, after 329 airframes were already built.) By modern standards, the early F-16s would still be in testing.
And USAF dissatisfaction with the F-16's (and F-15's) engine led to a bitter dispute with PW, leading to the alternate engine program. Eventually, GE engines power most F-16s today.
The F-14 is also imfamous for its bomber-derived engines, which performed poorly at high AOA.

So it's not just about safety, but also basic functionality.
In comparison, there's a couple hundred F-35s around today (~300, ~210 in the field, ~90 coming out of production), more than the F-15C/D (~180), F-22 (~180), or F-15E (220+) fleets. (Some are already in service with the US Air Force and US Marine Corps, others are wrapping up testing, and still others are stateside training the initial cadre of pilots for various partner nations.) While most of them aren't in service, they're already at a more "advanced" state of testing than the F-16 was after it had already entered service.
Of course, besides safety and thoroughness, more testing/development is necessary because more complex aircraft have more things to test/develop.
4: Multiroles can save money and can provide more capability

I still have great difficulty in accepting that... Having fewer airframe types saves cost and/or development time, this seems evidently incorrect. - [from the updated question]

First, if two aircraft are similar enough, you might use the same aircraft to serve both roles. You develop one aircraft instead of two, theoretically cutting your development costs in half. Or you can use those savings to design a better plane. In practice, you might need to make some mods to suit different roles/customers, but the airframe and systems are [hopefully] similar enough to yield net savings (or a better aircraft).
This isn't unprecedented. The YF-16 and YF-17 both fought for the same US Air Force program, but the USAF took the F-16 and the Navy developed the YF-17 into the F-18.
Second, the F-16 already does this. It already performs a variety of roles previously flown by several different types of aircraft. It's used for everything from close air support, interdiction/deep air support, and suppression of enemy air defenses, to air superiority and recon.
The Super Hornet is also a potent multirole platform. Even the F-15E Strike Eagle, built for long range interdiction, has basically the same air superiority capability as the F-15C. Even the F-14 earned its "Bombcat" moniker. In fact, most modern and [surviving] legacy fighters are multirole: F-15, F-16, F-18, F-22, F-35, Su-27 family, Gripen NG, Rafale, Typhoon, J-10, J-20, etc.
Multiroles are flexible and increase total available capability. Example:

Say Plane A (air superiority) does "100" air superiority and 0 ground attack.
Say Plane G (ground attack) does 0 air superiority and 100 ground attack.
Say Plane M (multirole) does 75 air superiority and 75 ground attack.
Say you buy 100 planes. You have two options:

.
                          | Option 1    |  Option 2
                          | single-role |  multirole
--------------------------|-------------|-----------
number of Plane A (100/0) |   50        |    0
number of Plane G (0/100) |   50        |    0
number of Plane M (75/75) |    0        |  100
air sup. capability       | 5000        | 7500
ground.  capability       | 5000        | 7500

The multirole Plane M may not be as good as A or G in any specific role, but you get more capability overall. But if you build multiroles, you potentially have 100 planes available for each role.
This works because missions change. On Day 1 you might need a lot of air superiority, and on Day 2 you might need a lot of ground-attack. Well, with only single-role fighters (option 1), half your fleet is useless on both days. But with multiroles (option 2), all of them are useful on both days. (Missions can even change on the same sortie, eg an interdiction group defends itself against opposing fighters before proceeding to their target. F-16 strike fighters that can defend themselves can be more efficient than always assigning "just in case" F-15 escorts.)
This is even more true if you have more roles. If you have 10 different roles, you can only build 10 planes (average) for each role (in the single-role option). So up to 90% of your fleet might be useless on a particular day. (This is obviously an extreme example.)
But even at the least-optimal point (max A, and max G), the multiroles still provide good capability (7500) compared to the single-roles (10,000). The single-roles' capability will vary between 5,000 and 10,000 (depending on day), whereas the multiroles can always bring 7,500.
There's an exception. If you know beforehand you always need "5000" worth of air superiority, then yes, it's more efficient to build 50 air superiority fighters. But A) it's hard to know that beforehand (predicting the future), and B) that number will change over time regardless. But if you know you'll always need at least "1000" air superiority, then it's more efficient to buy 10 air superiority fighters (actually more than 10, depending on expected use). In practice, you'd build at least 10 air superiority fighters and give then some multirole functionality.
(There's another exception. This model assumes all Air Superiority or Air to Ground capability is identical, regardless of source/type. Obviously this isn't always true.)
Notice the break-even point in the example above. Plane M was 75/75, but if it was less capable (50/50), then Option 1 and 2 both offer the same available capabilities. So the multirole plane must be competent in its typical roles, otherwise the fleet composition is inefficient. On the other hand, the multirole plane doesn't have to excel at its typical roles, it just needs to be competent.
Thankfully, multirole fighters can perform a variety of roles very well just by swapping payloads. Take the F-16 for example. Need defensive counter air? Load up the AMRAAMs. Need CAS? Grab nav/targeting pods and load some JDAMs/LGBs. Recce? Photo-recon pod. SEAD? HARMs, decoys, and jammers. Anti-armor? Mavericks and SDBs. Antiship? Harpoons. Don't forget the fuel.
Recall how missions can change mid-flight. Those self-escorting F-16s are performing both roles simultaneously, say 25/75, so their total capability being used is 100, and fleet capability is 10,000 (equal to the single-roles on their best day or 2x the single-roles on their worst day).
The F-35 can perform multiple roles simultaneously. They can escort themselves, find targets themselves, strike a ground target, jam enemy aircraft and ground radars, and even take out enemy SAMS, all the while acting like mini-AWACS/JSTARS for friendlies. Say that's 75/75/75/75/75/75, or 450 total per aircraft and 45,000 for the fleet.

That's part of the value of multirole stealth fighters. They need far less support.
 (Image source: Beyond the "Bomber": The New Long-Range Sensor-Shooter Aircraft and United States National Security - Lieutenant General David A. Deptula, USAF (Ret.), 2015.)
That's partly why you see the F-35 winning 20 vs. 8 fights and racking up >20:1 kill ratios at Red Flag:

#5: [Multirole example] The F-35
[This section really deserves its own question/answer, but I'll abbreviate it here.]
Cost
The F-35A (\$94.6 million (FY16\$)) costs less than the Typhoon, Rafale, Gripen NG, and Super Hornet. In 2019, it'll cost a touch more (\$80 million) than a Block 50 F-16 (\$65-\$80 million).
Capability
Compared to the F-16, Hornet, Super Hornet, Harrier, A-10, Rafale, Gripen, and F-117, the F-35 is more capable in almost every relevant aspect. It has the best radar, best EW suite (probably), and best IR sensor suite. It has the best range and carries the most payload. It has the "superb low speed handling characteristics and post-stall manoeuvrability" of the Hornet and the acceleration of an F-16 (a 'Hornet with four engines,' remarked one pilot). At equivalent combat loadings, the F-35 is faster and accelerates/climbs more quickly. Sensor fusion and network integration provide excellent situational awareness (perhaps second to only AWACS) and greatly facilitate coordinated strikes.
Even versus the Raptor in air-to-air, it's not clear the F-22 would dominate. Some F-35 systems (the APG-81 radar, ASQ-239 EW suite, AAQ-37 DAS sensors) are direct upgrades of F-22 systems (APG-77, ALR-94, AAR-56). The F-35 radar ground mapping and targeting capability was actually backfitted onto the F-22. The F-35's EW suite has detected and jammed the F-22's radars. It's also twice as reliable and four times cheaper than its predecessor on the F-22. And the F-35's EODAS evolved the F-22's AAR-56 into much more than a missile launch detector, also providing ground-fire geolocation, weapon cueing, and situational awareness IRST (the famous "see through the cockpit floor"). Test pilots and USAF officials have also remarked that the F-35 is stealthier than the F-22.
The F-35 also has an integrated IR search and track system and helmet mounted cueing system. Both were canceled on the F-22. The F-35 will also carry 6 internal AMRAAMs (same as the Raptor) or 4 internal MBDA Meteors.
Development time

F-16: 2 years for demo (1972-74), 4 years to first flight (1972-76), 8 years to service entry (1972-80)
F-35: 5 years for demo (1996-2001), 10 years to first flight (1996-2006), 19 years to service entry (1996-2015)

Overall, F-35 development ostensibly took 2.5 times longer than F-16 development. Given the tremendous amount of new technology, it's notable that development time was comparable to other modern fighters, which also average 20 years (see far below) despite being far less technically challenging.
By running a joint program, the JSF eliminated a lot of potentially redundant system RDT&E and reinvested those savings into more advanced systems (and more systems). Eg, instead of designing three different radars, they designed a single (more advanced) radar---avoiding reinventing the same radar twice over, avoiding three separate test and validation programs, and avoiding managing three separate programs.
#6: Minor points/additions
1.)

I still have great difficulty in accepting that...
A reason would be the complexity of the problem, which is very often quoted. All aerospace problems are extremely complex, that is nothing new. But now nobody can tackle them anymore? That was the basis of my question.

I think the complexity has simply grown faster than the tools' ability to keep pace.
I think with modern tools and processes, it would be very easy to out-design any plane from before 1980.
2.)

You only do these new programs every so often, there's so much of a
  backlog of stuff you want to get done---you throw too much at it. You
  want to do all the new technology, all the new manufacturing
  processes, new tools, new everything all at once. It makes the
  complexity exponential. [So] You need to find things to advance
  outside of these programs to get yourself ready for these programs, so
  when the opportunity comes up... the technologies [will already be] in
  the market, so you know what you're doing so you can execute...
  instead of "it's been so long that we need to start at ground zero
  [with] a new program plan, a new organizational structure, a new
  teaming"---all that at once makes it hard to execute. - David Kusnierkiewicz, Mission Systems Engineer (NASA), Johns Hopkins University Applied Physics Laboratory. Speaking at AIAA ("Whatever Happened to the Four Year Airplane", @31:00)

Many reasons:

Modern aircraft are vastly more complex

Scale.

An F-16 weighs as much as an B-25 (9 tonnes). An F-22 (20 tonnes) weighs 60% as much as a B-29 (34 tonnes).

Software.

The F-16C had 150,000 lines of code. The F-22 had 2 million lines of code. The F-35 has 8+ million. The F-35's logistics system has 24 million lines of code.
Automation/software is basically narrow AI, replacing several extra crew members: radar terrain mapping, analyzing ground targets through multiple sensors (optical, IR, radar), automatic target recognition, missile approach and warning, electronic attack, defensive countermeasures, etc.
Even engine start up is simple, "requiring just three switch selections, one each for the battery, integrated power pack and the engine...  Initiated by a button in the cockpit, the [vehicle systems built in test (VS BIT)] self-tests almost every function imaginable on the aircraft... After 90 seconds, if there are no problems, the aircraft declares itself ready for flight" (Mark Ayton).
In comparison, the SR-71 is practically just an airframe with a camera and jammer.

Systems

Systems are much more complicated than the basic structure:
A "stealthy" low probability of intercept AESA radar, distributed aperture system for missile approach and warning and 4pi steradian observation, helmet mounted display, electro-optical targeting system for IR search and track and ground targeting, electronic warfare suite (which, in the F-35, is reputedly much more complex than even the radar), "stealthy" low probability of intercept and high data rate comms, electro-hydrostatic actuators (each actuator is self-contained rather than relying on an aircraft-wide hydraulics loop), and of course stealth (from the LPI comms, LPI radar, skin, to the nozzle).
Sensor fusion. Then you must fuse all those sensors and comms together and integrate with the rest of the fleet so that everyone sees the same picture. If a lone drone spots a distant fighter/tank/missile, everyone immediately sees it as well. Sensor fusion is responsible for much of the system/software complexity. But you cannot divorce the systems from the aircraft. They are part and parcel of the 5th generation experience... and thus responsible for the incredible capabilities necessary for the future.
In other words, much of the complexity is necessary to deliver the requisite capabilities.

More development and testing before service entry

Modern safety standards
Earlier aircraft entered service before many of their iconic systems were finished. In modern practice, the first few hundred F-16s would still be in development/testing, rather than pushed into service before even the airframe and control laws were completed.
For example, in just its first few years of service, the F-16 had 50 crashes. It was nicknamed Lawn Dart for a reason. In contrast, the F-35 has had zero crashes and only two Class A mishaps, once when they flew too hard without first breaking in the engine and once when they tried starting the engine with excessive tail wind.

The physics are better understood

The 50s, 60s, and 70s saw a flurry of new designs as new frontiers were explored. These were poorly understood, so as basic knowledge accrued, older designs rapidly became obsolete. And since airframes were relatively simple and manpower high, designs evolved incrementally but continuously (rather than in discontinuous leaps today). Opposite NATO, the Soviets were doing the same and thus engendered continuing competition.

Twenty years is pretty typical for modern aircraft development. The F-22, F-35, Typhoon, Rafale, Hornet (including 8-10 years of YF-17 development), and even PAK FA all took (or will take) about 20 years from start to IOC.
A quick note on the SR-71. It wasn't developed in two years. It was derived from the Lockheed A-12, which flew before that SR-71 mockup was even shown. The A-12 program began in the late 50s, and the J58 engines started development even before that, initially for the P6M strategic flying boat, which first flew in 1955.
A quick note on O2 issues. A lot of high performance jets have had recent hypoxia issues, not just the F-35, including the Hornets, Super Hornets, T-45s, and [infamously] the F-22s. The F-15, U-2, and SR-71 also had their fair share of O2 issues.
Just for fun: AIAA AVIATION 2015, "Whatever Happened to the Four Year Airplane"

On the software issue: does it have so many lines of code because it must be the multifunction fax-printer-scanner-toaster-wafflemaker from @Criggie's comment?

So if the problem is: aircraft become more and more complex, why is the solution then not: split up the complexity in more airframes, which can each be optimised for their task?

Yes, splitting up the complexity would certainly help.  It's been suggested that if the US military had gone for separate aircraft for the ground-attack, air-superiority, and carrier fighter roles instead of a universal aircraft like the F-35, they'd have all three of them done in less time and on a lower overall budget.

@Koyovis The main reason for "so many lines of code" is "because you can". Processors get faster, memory gets cheaper, so there is no incentive to economise - just stitch together an ever-increasing number of (supposedly) standard and (supposedly) reliable existing packages, and ignore the fact that you often end up with 57 varieties of the same basic functionality. Then, the safety and reliability guys get involved, and insist you write 10 lines of code which serve no more purpose than one, just to meet some box-ticking "quality standard" they invented...

@Koyovis - No, most of the systems (and their softwares) would still be there even if you made 3 separate airframes to succeed the F-16, F-18, and AV-8B. Notice that all three are also multirole. The F-35 gets a lot of flak, but it's the most cost effective multirole fighter in the world. It's extremely capable in CAS, interdiction, and air superiority (second only to the Raptor). It's also one of the cheapest modern fighters.

@Mark - I remember that paper (and its rebuttal). It was 2 years old at time of publication. And it's based on 2010 SAR data, right when the program was being reworked. Ever since, the F-35 has been pretty much on time and on budget.

I still find it hard to see that the solution is to combine the complexity of three multi-role aircraft into one, and then mention the complexity as the reason that development takes so long. When we say "the most cost-effective multirole fighter", what can we compare it against?

@Koyovis - JOINT: Then you'd have 3 complex development and test programs. In theory, if the a/c are similar enough, you can use one a/c vs. 3 a/c with overlapping/redundant RDT&E. In practice, lots of cousin parts but the most complex components are common to all. COST: The F-35A ($94.6 million (FY16$)) costs less than the Typhoon, Rafale, Gripen NG, and Super Hornet. In 2019, it'll cost a touch more ($80 million) than a Block 50 F-16 ($65-$80 million). It's more capable and survivable than all of them. Even versus the Raptor, it's not clear which is dominant.

A fine answer. Would you mind changing "a/c" to aircraft? I keep wanting to read it as air conditioning.

Under your scale point, not everyone (myself included) knows how much a B-25 & a B-29 weigh. I'm an aviation fan, but I'm not an encyclopedia, so if you included those values, it would help make your answer even better.

I agree that a modern platform is more complex than an old platform - it always is.

That number of lines of code scares the hell out of anyone who has ever written code.  24 million lines of code approximately equals 48 million bugs.

Update contains very good points, particularly on the multi-role.

Just found out from Software Engineering Stack Exchange that Firefox has 20 million lines of code. That puts things in perspective.

@Koyovis - http://www.informationisbeautiful.net/visualizations/million-lines-of-code/ has a couple popular comparisons

Interesting link, 8 million lines of code compares with the Chevy Volt. I've updated the question.

@Koyovis - Ugh, I kinda regret bringing up MLOC. LOC is a poor metric of sophistication at even the best of times, to say nothing of completely different domains with completely different requirements for speed, reliability, and security, I brought up the F-22 (2 MLOC) and F-35 (8 MLOC) because some of their systems were direct predecessors/descendants (and obviously they're in the same domain), so the comparison is more apples to apples. But absolute number is less important than the relative change. Designs are complexifying, yes, but by how much exactly? What metric? I wouldn't say.

@Koyovis - How bad is SLOC (source lines of code) as a metric?
https://stackoverflow.com/q/3769716. "Measuring programming progress by lines of code is like measuring aircraft building progress by weight." -- Bill Gates (supposedly from his book Business @ the Speed of Thought)

Then why was it mentioned as justification for a long development time? And are we measuring progress, or size? We do categorise aircraft by their weight, in fact that was point 1. In your original answer.

Let us continue this discussion in chat.

I would like to argue the point that the F-35 has more stealth capability than the F-22. The Raptor was primarily designed for stealth super-cruise and in all situations has a much smaller EM profile than the F-35. If you are certain I am in error, could you please tell me where you got that information?

@Jihyun - The Raptor... has a much smaller EM profile than the F-35. Ever since the F-35 began real-world testing [using production-representative materials and techniques] either on the pole or in the air, US officials have explicitly and consistently remarked that 'the F-35 was stealthier than the F-22.' These officials include the commander of US Air Combat Command (Gen Hostage), head of the JSF program JPO (Lt. Gen. Bogdan), and test pilots. They've reiterated this a number of times over the years in interviews and articles. A compilation of some of those remarks: https://redd.it/30fa43

@Jihyun - However, note that these remarks are deliberately and obviously vague, citing neither the aspect nor band (no surprise)... nor weather, operating mode, ECM environment, material condition, material generation, magnitude of the difference, etc. Divining the spirit of these remarks, we may conservatively interpret it to mean "the F-35 is modestly [but noticeably] stealthier in the most relevant aspect and band (ie X-band, frontal aspect)." A less charitable interpretation may assume the F-35 must rely on its EW suite to realize such gains, but there's no obvious indication of such.

@HephaestusAetnaean I realize your point. Yes, if all those factors are considered, I too assume it could be possible to see how the F-35 could be more 'stealthy' than the F-22

In the age of computerized design, drafting, testing and milling, we can develop products faster than ever before. It's definitely not technology slowing down development.
When we develop a plane for the future, whether it's for the Air Force or commercial aviation, we tend to focus on planning, and developing plans for the future. When Boeing and Airbus developed the 787 and the A380, they both had to forecast into the future the best way to spend their money to meet the demands of today and tomorrow. Each company took a gamble on whether airlines would prefer a hub and spoke model or direct flights. Similar planning happens with the US Air Force. That long-term planning does not always emphasize faster and cheaper.
In the case of the US Air Force they want planes that are fast, advanced and have no match in the sky. Others have mentioned some of the drawbacks and advantages with programs like the F-35, I am going to focus on what can be done today.
My example of the development speed possible is the Textron AirLand Scorpion. This is a composite fighter, designed with off-the-shelf parts, leaning heavily on technology developed for Cessna, who is the actual frame builder. It was designed to be a light attack and intelligence, surveillance and reconnaissance (ISR) platform. It was proposed in 2011 and had its first flight in late 2013 and sells for $20 million for the plane. That's under two years of development.
This plane is no match for the F-35 in terms of speed or flexibility. The plane does not do VTOL, carrier landings, the maximum speed it 518 mph, the ceiling is 45,000' and the range is under 3,000 miles. The cost and time for development did not include things like the ejection seat, the flight controls which are borrowed from other developments. If the Scorpion incorporated all of those aspects in development, the price and development time would have increased dramatically.
This plane is low cost and can handle training or defense. It shows what could happen in development in the 21st century when you remove a lot of politics, planning and other requirements from plane development and focus on building something low cost, low maintenance and reliable.

More information:

http://www.scorpionjet.com/
https://en.wikipedia.org/wiki/Textron_AirLand_Scorpion

An earlier example of a similar concept (cheap, proven technology, no fancy stuff) was the F5 Tiger.

Very good point. From the article in The Economist referenced in the question: "Mr Pugh also identified another intriguing trend: the race for bigger, better weapons is fiercest in peacetime but tends to fall once war actually breaks out. At that point, he argues, quantity takes precedence over quality. "

@Koyovis what mostly becomes important in wartime is rapid production of replacement assets to replace those lost in combat. That and ease of use so the system can be used by new recruits with only limited training. You still want to outperform your opponent, but numbers become more important than longevity of a single system as most of those systems won't last decades in wartime, they last days or weeks at best on average.

This is just an additional point, but a bit more than a comment.
In the late 60s there was still a cohort of design/test personnel whose skills and attitudes were formed during WWII and the early stages of the cold war.
On the test side, the likes of Chuck Yeager and John Stapp were still active.  Their careers were built on taking personal risks of a type that would be unthinkable today.
The designers don't tend to be as famous but Alexander Kartveli led the design teams for the P-47 Thunderbolt, the F-84 Thunderjet and the F-105 Thunderchief, and not as a manager but as a designer, having been involved in plenty of earlier designs.  How many people have experience of designing multiple aircraft these days?
Of course the need to integrate ever-increasing amounts of first electronics, then software increases the complexity. This increases the workforce to a larger-than-optimal size, which further slows things down (especially as it involves subcontracting).

The same arguments apply to civil aviation and space.  In all these cases sales consist of small numbers of expensive units, and the risks of failures leading to disaster are high.  For smaller, more mundane and commonplace things like cars, it's easier to tweak or evolve existing designs, adding features based on the market; in these cases even multiple failures are unlikely to be catastrophic.

The complexity increases even more when politics decides to make the project multi-national. Now you have national egos (on the political side!) hijacking the project at their whim. The result is more duplication of work and endless meetings. Look at Augustine's Law XLVIII where that leads to.

After the TSR2 was cancelled, many British engineers left the company, many even emigrated. So for the next aircraft a lot of new engineers had to start from scratch. (The arrangement for cancelling TSR2 included shredding all drawings and destroying all models and prototypes. It was a political decision.)

@RedSonja your brackets include a good point -- cold war paranoia led to a mindset that discarded hardwon knowledge

One other factor that has to be considered: The government oversight of military projects has also risen in complexity. The paperwork and approvals necessary are staggering. A good deal of the trouble with the F-35 is changing requirements. Its mission requirements have changed a lot since the early 2000s when the prototype first flew. The 'see-through helmet' was not part of the original prototype. And, to a degree, the global situation changed during the F-35's gestation period.
One reason Lockheed was able to develop the P-80, P-104, and U-2 so quickly was - minimal government oversight on those projects, and a simpler situation to deal with.
Another reason was Kelly Johnson.

Specifically in the US, Congressional oversight can not be understated. Constantly changing funding availability, directed expenditures (buy X from Y), changing production rates, GAO Audits, investigations over minor performance issues all consume a huge amount of time. And Congress is incapable of dealing with the concept of continual improvement. If it isn't perfect, you can't get approval for full rate production, even if the 'shortcoming' can be fixed downstream with a simple field update. So the program continuously languishes in limited production where everything is more expensive.

The F35 program generates something like 10,000 pages of documentation per week.

And inevitably the red tape which leads to projects taking longer indirectly (through the increased timespan) leads to changing requirements which leads to even more red tape. Both lead to needless expense of a lot more money too, and the cost of a project spirals completely out of control to the point you can buy a single F-35 for the cost of almost a squadron of F-16s yet the aircraft is barely more capable (and that's an optimistic estimate).

Don't forget the hours (years) of flow simulation , dynamic response, FEA, and other computer simulations that modern vehicles require.  These are necessary and good, since they reduce testing cost and ultimately lead to more robust products at a fraction of real-world testing.  They're not without their drawbacks (high initial computer cost, software and training, etc.) but on the whole it's much better than building a $40m prototype and watch it crash just because someone forgot to convert lbf to kg.

True. I wonder why the process takes so lomg though, since the simulation and CFD can be done before the first machine is built.

Yes, but it mostly works the other way. Prior to CFD and CAD analysis, actual wind tunnel tests (many thousands of hours) and static tests had to be done. CFD and CAD are supposed to be a cheaper and faster way of design. Yet the original question asks why doesn't it happen in practice, despite these advances.

Technology-Life-Cycle
In the first decade of the 20th century planes were invented and started flying with piston-engines, in the middle of the century we got the advanced turbofan-engines. Both requried and allowed for a lot of new planes and designs and fast iterations with improvments, because they advanced everything. Bascially we have seen "only" improvements since then, first bigger improvements and now smaller improvements. And improving an already well working thing gets harder and harder over time.
If we get a new game-changer in flying-technolgy we will probably see soon a lot of new planes and a second wave with improved new planes and so on.
Beside that, the already mentioned points are right. Especially the cold-war is over and therefore the need for huge fleets of new planes is small. Computers make everyting comfortable but a lot more complicated. And the customer want a multi-role-planes, which makes things even more complicated.

Aerospace has always been complicated. What makes present day problems more complicated?

First planes were not built for war, so engineers attached guns and it became more complicated, because you now hit your own propeller (either you sync both or built-in the guns into the wings, which weren't designed for guns...). And it goes on with radar, gps, autopilot, fail-safe-systems, retractable landing-gear and finally the F-35: STOVL -> COMPLICATED^2

Feature Creep
This has been ongoing for decades: Fewer types for more and more roles. Where military planes were originally designed for a narrow set of missions, there has been the tendency to replace multiple types with a single, multirole type.
Whats makes this so problematic for the designer is that different roles have wildly different requirements on the planes abilities:

The Navy demands a plane that can operate from their carriers
The Army demands a plane for the strike/close air support role
... and a tank killer, too.
The Air Force demands an interceptor/air superiority fighter

Now each of these roles has demands that more or less directly conflict the demands of another role. You end up designing a jack of all trades plane, trying to reconcile dash speed, long range, long loiter time, reinforced airframe for carrier use (add folding wings for space), high penetration power anti-tank gun.
To cram all that into a single plane you need to make compromises that will not be ideal. To make up for the shortcomings of the compromise you need to go to the very edge of technology to at least cancel out some of the performance loss that came with the compromise (e.g. you need more engine power because your airframe isn't primarily designed for high speed, you need larger tanks than a pure fighter would need and so on). All this tends to add subsystem after subsystem, complexity and weight.
To counter the ever increasing weight (and airframe size) demanded by all the features, the only choice is to go for as compact and light systems as you can make them. Designing at the very edge of what technology allows, is costly. Nobody has done it before in exactly that way, no industrial supply chain for the desired materials and tools exists. All this adds to developments and procurement cost.
At the same time, your budget is limited for any given fiscal year, if you overrun the budget you'll need to get more budget, which will add burocratic delays and so on. All in all this adds up to steadily increasing cost in both time and money.

Why then are there not multiple types, each optimised for their own task?

@Koyovis Fewer types simplifiy military logistics and tactics. Need a fighter? Arm as figther. Need strike aircraft? Arm with strike package. The tendency is to do more tasks with fewer units. Financing and burocracy also have some impact, its easier to get one program approved than three.

This is the most important answer imho. This is what slows you down. The previous guy sitting in the customer's office wanted a cup holder in pink, now the new guy wants a bottle holder in blue. The new guy earns kudos by finding things the previous guy "got wrong" and coming up with an "improved" version. Sometimes it's just a new fad they saw some NATO partner got. Every one of these changes is waved through by our management - we earn money that way - and dumped on us. This is true of all military manufacture I have ever dealt with.

The first jet fighter only had to be better than a none jet fighter.
The next jet fighter only had to be better than the first jet fighter for the  single job it was created for.
Lot of different types of military jets were created that were a little bit better then what come before them, for the one task they were designed to do.
Then it was decided that it would be better to have fewer types of jets, and that they had to be able to do everything all the different jets they are replacing could.    Then it was decided they had to be better then all jets they were replacing in every way.
As the older jets were still working, getting a “perfect”, “do everything”, “keep even one happy” jet was considered more vital than keeping the design time or cost down…..   But then as it took so long, and the next design may not come for anther 20 years, the requirements were increased even more....

The answers above have provided very good insight into the issues associated with designing a new fighter jet. The question was particularly about the long development time, twenty years in total. Distilling all answers, a conclusion may be reached, but I'd first like to address some of the particular items raised.
To start with what I don't reckon the issue is, based on  order-of-magnitude comparisons:

Not stealth. The F-35 is compared with the F-16 with regard to observation by radar. This video mentions how stealth was incorporated into the SR-71 already - the SR-71 of the question! Stealth technology is over half a century old! A bit further on in the clip it is mentioned that the SR-71 has a radar signature 100 times smaller than that of an F-14, which is half the size.
Not: ever increasing better arms of the adversary. Arms races and their consequences in times of the American civil war were already mentioned by Jules Verne in his 1865 book From The Earth To The Moon. Again in the video referenced above, the weapons officers are describing jamming the radar of weapons systems locking on to their plane. The ever increasing arms race has been an ever increasing issue for over 150 years. Yes the issues are growing faster, but the solutions are standing on the shoulders of ever growing giants.
Not: the number of software Lines Of Code. Although a bug in aeronautical/ weapons systems software has graver consequences than a bug in Microsoft Office, it is not the number of lines per se. The F-35 has 8 Million Lines Of Code (MLOC) on board, comparable to a Chevy Volt. F-35 logistics has 24 MLOC, comparable to Apache Open Office. That represents a sizeable amount of man hours and development time - implemented incrementally, like the weapons systems are. Aeronautical and weapons systems software
Not: the problems being so complex. It's aerospace! The question boils down to: why could incredibly complex, novel problems be solved so much faster in the past. Yes the mission of the SR-71 was flying fast with a camera, while not being shot down by whichever advanced weapon available. Apollo 11 only had one mission as well, what has that got to do with the price of fish? It was accomplished in eight years, less than half the time required to put the F-35 into service.

What then does contribute to the long development time? The question compares the present day situation with over half a century ago, when full scale warfare between nations was still a vivid memory, and nations were still armed to the teeth. The high tech nations have fortunately not been waging war with each other ever since.
This article which appeared in a 2010 issue of The Economist adresses the increasing cost of weapons systems. A quote:

Philip Pugh, author of “The Cost of Seapower”...also identified
  another intriguing trend: the race for bigger, better weapons is
  fiercest in peacetime but tends to fall once war actually breaks out.
  At that point, he argues, quantity takes precedence over quality.

So one can conclude that it's a peace-time general trend in all weapons systems that they should be perceived as superior. Not tested by war, their deterrent value may be as important as their actual destroying capability. And that is a good thing.
The F-35 turns out to defeat Augustines law XVI: In the year 2054, the entire defense budget will purchase just one aircraft. This aircraft will have to be shared by the Air Force and Navy 3-1/2 days each per week except for leap year, when it will be made available to the Marines for the extra day. I greatly enjoyed learning about Augustine's laws from @Peter Kämpf's answer - it looks though as if he was just signalling an age old peace time trend.
Like stated in the end bit of the OP question, I don't want to knock the end product, the F-35, which ultimately turns out to be a competent weapon that defeats wider cost increase trends. But why did it take so long, and why did it accumulate such bad press in the process?

Opinion ahead
It is clear that all factors that were driving urgency are not present anymore, which is a good thing. It is much easier to live in peaceful times. Also, the enemies became a-symmetrical and different sorts of weapons were required. We don't have the fire breathing program managers anymore, bred by war-time development of ever better weapons. Like Kelly Johnson, who's record does not cease to amaze. He developed the Starfighter in 1 year, nine years after WWII with its Spitfires.
It may just be that fast jet development is in a dormant stage now and that everybody understands that. It's a good thing that the capability is kept afloat. The F-35 will turn out to be a good and cost effective machine, that just took a while longer to develop. What's two decades in a lifetime, right?

Apollo was a success despite, not because of, NASA. When NASA got involved, you had cost overruns and deadly accidents. Only by leaving most of the work to contractors and directing them at arm's length could the program succeed. The prime reasons for success was a clear motivation of all involved (Beat the Russians!) and a clear goal (man on the moon by the end of the decade). In todays projects, motivations are diverse (let's try to blame the other guy, mostly) and goals even more. This is actually good, because it shows that threats have vanished.

The F-35 is compared with the F-16 with regard to observation by radar. The F-35 is actually much stealthier than the F-16 and apparently even stealthier than the F-22. If you'd like, I can dig up some pilot and program officials' testimonials.

the SR-71 has a radar signature 100 times smaller than that of an F-14, which is half the size. The comparison is a little unfair.
• A) The SR-71 actively tried to lower its RCS. The F-14 didn't even bother. It's very easy to balloon your RCS if you're not careful, and back then people simply didn't care [most thought RF VLO was impossible, so why bother]. In LO terms, a 100x reduction is relatively easy to gain/lose.

• B) A mach 3 recon platform is naturally stealthier [than a fleet defense fighter]: streamlining and thermal loads alone demand a very clean skin, unblemished by external stores, pylons, pods, large control surfaces, huge bubble canopies, etc… unlike the "dirty" F-14 whose entire raison d'etre was lugging around 1000 lb missiles.

• C) This comparison isn't very flattering. The F-14 had a very large RCS, probably similar to (or greater than) the F-15 (~25 m^2). For comparison:, B-52 (~100m^2), F-16 (1+ m^2), eurocanards (<1 m^2), F-22 (~0.0001 m^2). That RCS grows even more when you add external stores (which the SR-71 didn't have to).

• D) size has relatively little effect on RCS. Sometimes, greater size decreases RCS.

it seems simply a matter of sub-optimal program management. The success of the SR-71 can be contributed to the excellent program management skills of Kelly Johnson - A)* Back then, most aircraft development programs progressed quickly, not just Kelly Johnson's. Were he alive today, it's not clear he would necessarily have done a better job (for example) than Lt. Gen. Bogdan in managing the F-35 program. B) That statement implies all countries and all companies acquired sub-optimal program management and that they all acquired it at roughly the same time.

C) I submit an alternative hypothesis: The management and design tools have grown substantially since the 1950s, however they simply haven't grown fast enough to keep pace with increasing complexity.

@HephaestusAetnaean some fair points there, I'll amend the answer.

If you want to get into the specifics, the Government Accountability Office has repeatedly produced reports on the state of the F-35 program and made corresponding recommendations to the DOD, most of which have not been followed. A decent place to start is last year's GAO-16-390 (pdf), “F-35 Joint Strike Fighter: Continued Oversight Needed as Program Plans to Begin Development of New Capabilities”, which starts with a background overview of the history of the program and includes links to previous reports.
Short version: the DOD demanded the F-35 incorporate a raft of new technologies, many of which were not fully understood, and which it was wildly overoptimistic about, then rushed it into testing without adequate R&D and into production without adequate testing; when this was pointed out to them, the DOD spent 2001-2008 in denial and 2009-present reducing procurement and lowering production rates to cope with the resulting cost overruns.

While requirements for "new technologies, many of which were not fully understood" could be the reason for the long development time of the F-35 it doesn't explain why other aircraft suffer, according to the OP, from the same problem.

The article mentions in the introduction that "...we're nearing end of development." In 2016, 20 years after the contract for development was issued.

It's an interesting read. "As we have previously reported, DOD began the F-35 acquisition program in October 2001 without adequate knowledge about the aircraft’s critical technologies or design. "

"Not fully understood." But that's true of basically any new technology you're developing for 20 years in the future. You can't innovate without risk.

@Koyovis - Some context: GAO's literal job is oversight/playing devil's advocate. They're never happy with any program---even the most successful ones. From dozens of reports, I think I've seen them give a compliment just once. Of course they say "more oversight is needed." When have they ever said less oversight is needed? It basically amounts to "I don't need a job." --- If you read their past reports on the F16, they say basically the same things.

From the software development point of view, F35 has 8M lines of code on its own. 24M lines if you include all related systems. These code themselves takes a long time for developers to work on, not to mention testing them.

Is that one of the symptoms of lumping all requirements together?

@Koyovis No, little of that software is branch/variant specific. Most runs the core systems like radar, EW, and IR sensors.

@HephaestusAetnaean which all had to be developed from scratch?

@Koyovis - Better than developing from scratch three separate times.  But no, it wasn't all from scratch. Many systems were evolved from prior work and significantly upgraded: radar, EW, EODAS, RAM, and engine (F-22); EOTS (Sniper XR); helmet-mounted display (DASH III/JHMCS); laser IR jammer (NG, various); countermeasures (various); carrier landing system (MAGIC CARPET)... Even if the Navy and Air Force developed their own separate planes, they each would've developed almost all those systems anyway...

@Koyovis - ...and so would competing nations. They're developing their own IRST, advanced radar/EW/ECM, HMD, stealth materials, etc etc. The F-35 needs to be that advanced in order to stay ahead of the curve and stay there 20-30 years later. A lot of the F-35's core, defining capabilities (stealth+sensor fusion+networking) define 5th gen. You cannot/should not separate them from the aircraft... or any would-be replacement. Penny-wise, pound-foolish.


text:
Why are the positions of an aircraft's angle-of-attack vanes dependent on airspeed?
According to this answer to an earlier question of mine, the positions of the angle-of-attack sensor vanes on the A330/A340 are dependent not only on AoA, but also on airspeed (and, according to @ymb1's comment, this is true for all aircraft, not just the A330/A340):

1. AoA vanes are speed sensitive
An AoA vane is in essence a weather vane, but due to various aerodynamic interactions it's not perfect. From flight testing they would have worked out how speed affects the position, and based on that the sensed position is corrected by speed input.

This doesn't make sense - the airflow over the wing is qualitatively the same for a given angle of attack, no matter what the airspeed (as long as you stay below the first critical mach number, at which point you get shockwave formation and all sorts of other goodness), so how can the airspeed affect the readings from the AoA sensors?  Shouldn't the airspeed merely affect how long it takes for them to weathervane in the direction of the local airflow?

It's because the vane isn't weathervaning into the freestream, it's weathervaning into the local flow a few inches away from the skin, and because of the curvature of the nose, this flow changes with body AOA (and therefore speed) with some variation relative to the change in freestream AOA.  The Stall Protection Computer software will have calibration tables derived from development flight testing to compensate for most of this.

Assume straight-and-level flight for simplicity.  You are saying that for the exact same angle-of-attack, if the aircraft weighs A pounds and is flying at X miles per hour, the direction of the local flow a few inches away from the skin will be different than if the aircraft weighs B pounds and is flying at Y miles per hour?  Interesting.

No you're inferring more from the "speed" bit than intended.  The calibration tables are just {Vane angle X = True AOA Y} based on the difference between the actual nose vane angles and the test boom vane that is reading true AOA for the range of angles.  To the extent that the deviation between between measured and true AOA is speed sensitive, it's that the deviation isn't constant but varies with AOA, which varies with speed for a given configuration.  The calibration itself doesn't vary with speed.

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text:
Why is a 737 Original speed-restricted below 10 kft with inoperative windscreen heating?
According to this page on the 737's operational limitations, the Original 737s (737-100/-200) are limited to 250 KIAS below 10 kilofeet if the windscreen-heating system is inoperative:

Anti-Ice & Rain
[...]
737-1/200:
[...]
Window heat inop: max speed 250kts below 10,000ft. [My emphasis.]

Why is this?

"Kilofeet" is my new favorite term.

Coincidentally, there is a more general 250-kt speed restriction below 10,000 feet: https://aviation.stackexchange.com/questions/20837/why-are-speed-restrictions-imposed-for-flights-flying-below-10-000-ft

@DavidK Yes, most countries have such a restriction, but it is not a universal worldwide rule.

@Bianfable Good point, and apparently even when there is a restriction ATC can grant a clearance for a higher speed. In any case, if it is physically unsafe for the aircraft to fly faster than 250 kt below 10,000 feet, that is something I would want to know regardless of any other speed restrictions.

It's cold outside.

@EricHauenstein Mine too - apparently kilofoot "is a standard unit in certain fields." Primarily telecom, but also some aeronautics and atmospheric science.

To reduce damage in case of a bird strike.
The restriction is not only for the 737-100 and -200 models, the 737 NG QRH says:

WINDOW HEAT OFF
In flight:
WINDOWS HEAT switch (affected window) ..... OFF
Limit airspeed to 250 knots maximum below 10,000 feet.
Pull both WINDSHIELD AIR controls. This vents conditioned air to the inside of the windshield for defogging.

The reason for restricting the speed is that the windows are less elastic at lower temperatures and can therefore not absorb a bird strike as well as at nominal temperature. Since most bird strikes occur below 10,000 feet, the restriction only applies there.
I could not find a good source for this, but it is e.g. discussed on pprune.org:

Window heat also ensures the screen vinyl layer is kept elastic and resilient and better to absorb damage in case of a bird strike - not so if the screen is cold and hard.

and airliners.net:

cold windows become very brittle whereas warm windows have a degree of elasticity in them that makes them withstand birdstrikes better.

A new window was developed for the 737 and is installed on all models built since mid-September 2010. The technical data by PPG Aerospace list the following among the improvements:

Elasticity at low temperatures reduces potential for delamination and cold chipping

So low temperature elasticity seems to be improved. I do not know, if they removed the restriction from the QRH for the newer models.
Airbus also does not seem to have such a restriction. From pprune.org:

When I asked Airbus exactly this question their reply was that the windscreens had been tested at 350+ knots and cold.....therefore no problem!

My friend once told me that in the winter he thew a TINY pebble, gently and it landed on a car windscreen and shattered the whole thing. I wonder if this is why...

@Cloud I'd say partly, plus bad/old window with possibly invisible other weakening (like chassis pressuring a point), plus possibly harder throw than remembered/admitted.

Since most bird strikes occur below 10,000 feet  "!!!!"   Birds only fly to a couple hundred feet, but, I only now learned a few birds fly to astounding altitude:  http://wikipedia.org/wiki/Rüppell's_vulture

@Cloud. Shattering glass with tiny pebbles is a thing, assuming it's the right kind of pebble. https://www.elitereaders.com/car-thieves-ceramic-stones-break-car-windows/

@user3445853: Plus possibly bigger "pebble" than remembered/admitted.

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text:
At what angle-of-attack (sideslip angle) would a symmetric vertical fin plus a deflected rudder have a lift coefficient of exactly zero?
For rudder deflection angles of 5, 10, 20, 30, and 45 degrees, at what (negative) angle-of-attack does a fin-rudder combination (including dorsal fin if present) have a lift coefficient of exactly zero?
For the purpose of this question, define angle-of-attack in relation to the chord line of the fin alone, not including the deflected rudder.  If we ignore things like spiral slipstream, deflection of airflow around cabin, etc, it would be the same as the sideslip angle.
Loosely speaking, at this angle-of-attack we could say the force from the deflected rudder is being  exactly cancelled by the force from the fin, though in reality each influences the airflow around the other and the fin-rudder combination acts as a single unit.
To allow for a definitive answer, I'll specify to use the fin (including dorsal fin) and rudder from current -production Cessna 172 S, but feel to post an answer addressing the fin and rudder from any other aircraft.
Note that an aircraft could never sustain a sideslip angle that caused the fin plus deflected rudder to have a lift coefficient of zero, unless some other yaw torque due to something like asymmetric thrust or extreme adverse yaw from deflected ailerons was acting to maintain the slip angle.
Approximations are fine-- obviously an exact answer would involve a complicated computer modelliing project, or actual wind tunnel experiments.  My hope is that existing information relating to the lift curves of symmetrical airfoils with deployed flaps may be adapted to give an approximation of an answer to this question.

Despite specification, this is a very broad question. Obviously, for each combination of airfoil, relative rudder chord and other minor factors there will be 'angle of zero lift' for each deflection; it's just a matter of mundane calculations or testing. What information each of these random points can give you? (Say, NACA 0012, 25% rudder, 10° deflection -> -5° $\alpha_0$. So?) Trends may be interesting, such as this angle per deflection vs. relative chord, but that's not what you're asking...

Besides, "an aircraft could never sustain a sideslip angle that caused the fin plus deflected rudder to have a lift coefficient of zero" - why, this always happens in a sustained sideslip (even without adverse ailerons, fuselage interference etc.)

@Zeus - why do you say that?  I would say that in a sideslip in a Cessna 152, where you are pushing hard on the (let's say right) rudder pedal to keep the  rudder deflected, it's likely that the NET contribution of the rudder + fin is a yaw torque toward the right, acting against the leftwards yaw torque created by the fuselage.  (Basically I'm saying that the center of lateral area or effective center of aerodynamic yaw torque of the fuselage alone is likely well behind the CG, since the rear parts of the fuselage act at such a large moment-arm.)

Why do you include fuselage? You excluded more relevant things like "spiral slipstream, deflection of airflow around cabin, etc.", why should I assume that fuselage should be calculated? Its influence can be quite complicated. A slender body has its AC quite far forward actually, but when you include interference of other parts (wing, "deflection of airflow around cabin, etc"), there may be no AC as such. With fuselage, the exercise cannot be reduced to "lift curves of symmetrical airfoils with deployed flaps", so you either should exclude it or define exactly.

Here are two links to Tom Speer's homepage. They show the performance of a couple of flapped airfoils. They aren't symmetrical, but it doesn't matter for what you are doing. What you want to look at is the change in the AoA between adjacent flap deflections.
For instance, it the first link, the there is a series for -3 degrees flap and one for 5 degrees flap. Holding the coefficient of lift constant, you'll see about a 4 degree difference in AoA. Thus deflecting a smallish 20% flap is about the same as rotating the whole foil by half as much.
http://www.tspeer.com/NACA23012/N23012wflap.htm
http://www.tspeer.com/NACA23012/N23012wflap.htm
For a 50% flap, it can be as much as 80% effective. See also Tom's analyses of wingsail performance with various sized flaps at the same site. These are symmetric foils, but you have to do some extrapolation to run the lift down to zero.
Tom worked for Boeing, and has worked on numerous high performance projects including the America's cup wingsails and landyacht projects.

If you want an approximate answer, it is any time a steady heading sideslip is performed (rudder vs. resulting sideslip). It's approximate because the fuselage and ailerons also contribute to the yawing. But if the fuselage is only mildly destabilizing, the answer should be in the ball park.

Agreed- I guess I would tend to think in a typical light plane the fuselage is rather strongly stabilizing.  Maybe I am wrong.  Maybe another question for ASE.  (Example Zenair where there is virtually no fixed fin at all; obviously an extreme case.)


text:
Does downwash increase or reduce lift generation?
I’m wondering about the impact of downwash on lift generation. I've read that, because downwash creates lift according to Newton's third law of motion, increases in downwash due to greater AoA (especially when augmented by devices such as slots and slotted flaps, which use various aerodynamic effects to increase the amount of downwash generated) result in increased lift. But I've also read that ground effect increases lift by decreasing downwash, so I'm confused how this works. Can someone clarify the effect of downwash on the amount of lift generated and tell me whether I've got it right or not? Thanks!

This is a most excellent question. I've struggled with this for a while. From a Newtonian perspective, there must be momentum transfer from the flow to the wing in order for the wing to gain lift, which necessitates in the generation of downward airflow. Let's call this downward airflow downwash.
However, from the circulation theory of lift, which holds incredibly well for low Mach aircraft, downwash is the source of induced drag (note that this theory does not account for viscous drag or form drag from flow separation). Furthermore, this drag is the result of reduction in lift, due to downwash; increased downwash equals more reduction in lift and more induced drag.
Consider the elliptical lift distribution (which for all intents and purposes, can be considered a typical wing distribution for low Mach lift, without loss of generality), the downwash over and behind the wing is constant across the span of wing, and can be expressed as (Ref: Anderson, Fundamentals of Aerodynamics):
$$(1) : w=\frac{SC_L V_\infty}{\pi b^2}=\frac{C_L V_\infty}{\pi A}$$
where $w$ is the downwash, $C_L$ is the lift coefficient of the wing, $S$ is wing reference area, $b$ is the wing span, $V_\infty$ is the free-stream airspeed, $A$ is the aspect ratio.
Induced drag, for an elliptical distribution, can be expressed as:
$$(2): C_{D_i} = \frac{\pi w^2 A}{V_\infty^2} = \frac{C_L^2}{\pi A}$$

So what do we get from all of this? From equation (2), induced drag is directly proportional to the square of downwash for any aspect ratio. From equation (1), the lift coefficient is proportional to downwash. By increasing aspect ratio, downwash, and therefore induced drag, can be reduced asymptotically to zero, while the wing's lift coefficient stays unchanged.
In other words, while downwash is necessary for lift, it also results in (induced) drag; increasing the aspect ratio makes downwash more efficient at generating lift and reduces (induced) drag.
In ground effect, the exact same thing happens as the reaction from the ground makes downwash more efficient at generating lift. This is manifested, once again, from a reduction in actual downwash for a given lift coefficient.

Work on winglets is pointing towards removal of draggy turbulent areas from the wing.  Could it be that increased pressure under the wing is pushing downwash further aft?  Would this re-direction be less draggy, a bit more thrusty, or both?

@Robert Not sure what you mean by the first part. A winglet in the Whitcomb sense converts induced drag from the winglet into forward thrust. But winglet is always inferior to an equivalent span extension if there's no restriction on span.

"Removal of draggy turbulent areas" is consistent with laminar flow theory, "clean wings", golf balls, rear mounted props, reverse tapered trailing edges, rounded wing tips, Hoerner wing tips, not mounting engines (or munitions) above wings, mono wings, thin wings, just to mention a few things we all have at our disposal to build a better plane.  "Restriction on span": too bad 747 size seagull wings can't be built, or can they?

Downwash is behind the wing and is the result of pressure differences between the top and bottom of a wing.  Although the energy conservation bookkeeping says the plane goes up and the air goes down, the main driver of lift is pressure differential.  True to Bernoulli, the angled bottom wing slows and increases air pressure beneath the wing.  This is "bottom lift" that even simple flat plates have.
Airfoils also deflect air upwards and away from the top of the air foil, creating additional lift above the wing.  Downwash is created by the movement of air from higher to lower pressure as the wing goes by, filling the void where the wing was.  This constant process is known as circulation.
Ground effect may not be directly related to downwash, but may be indirectly, as the ground and the downwash stream may create enough of a "fence" to slightly raise the pressure under the wing.  A Cessna 172 has a wing area of $174 feet^2$.
$174 feet^2 × 144 inches^2/foot^2= 25056 inches^2$
A pressure increase of 0.01 psi from ground effect adds 250 extra pounds of lift!
Ground effect is also said to be caused by the wing tip vortices being disrupted by their proximity to earth.

So the lift gain by downwash is some kind of very small „addition” to overall lift that is mainly generated by pressure differential by Bernoulli? I asked about downwash in ground effect because in atpl books and atpl questions there is mentioned that in ground effect downwash is reduced, so the induced drag and then our lift is less inclined backwards and the overall lift increases. Am I getting this right?

It depends on what theory you wish to believe. As a pilot, ground effect is real.  Down wash is after the fact (of lifting the plane). And some say bottom lift is not Bernoulli, but momentum mv of the wing colliding with the air. I think any downwash hitting the ground is even more after the fact, and downwash itself does not create lift, it is the result of it.  However, if you look at a plane with an AOA of 12 degrees 20 feet off the ground, one may imagine a compression wave hitting the ground and bouncing back to the wing.  This "ground effect" makes sense as much as the other explanations

Strictly, the more wing lift is created the more the downforce on the air. They are equal and opposite forces.
Yes, the increased downforce usually results in greater downwash.
But if the ground is in the way then the downwash gets spread sideways and its net downward component is reduced. This raises the local pressure between wing and ground, increasing lift.
So in normal flight the downwash is a consequence of lift, while in ground effect the added lift is a consequence of downwash.